Biology Reference
In-Depth Information
Table 2
Output files from a SAT ´ analysis
Output file name
Description
myjob.marker001.sequence.aln
SAT´ alignment
myjob.tre
SAT´ tree
myjob.score.txt
ML score for the SAT´ alignment/tree pair
myjob.out.txt
Diagnostic messages
myjob.err.txt
Error messages. If this file is not empty,
check your settings and retry the analysis
myjob_temp_iteration_initialsearch_seq_alignment.txt
Starting alignment
myjob_iteration_initialsearch_tree.tre
Starting tree
myjob_temp_iteration_0_seq_alignment.txt,
myjob_temp_iteration_1_seq_alignment.txt, etc.
Intermediate alignments
myjob_iteration_0_tree.tre, myjob_iteration_1_tree.tre,
etc.
Intermediate trees
myjob_temp_name_translation.txt
Taxa in intermediate trees and alignments
are renamed according to this translation
table. The temporary substitute name
for a taxon is shown on one line,
followed by its original name, and then
a blank line
The analysis used a job name of “myjob” and the input file was named “sequence.fasta”
1. If additional time and computational resources are available, an
extended, more thorough SAT
´
analysis can be run. To do this,
run the following steps.
2. In the “Quick Set” drop-down menu, select the “SAT
´
-II-
ML” option.
3. In the “Decomposition” drop-down menu, select the “Cen-
troid” option.
4. Proceed with
steps 7
through
10
from the “Basic Analysis”
sections
8.3
and
8.4
, but be sure to pick a large enough number
of iterations.
8.5 Advanced
Analysis: More
Iterations Desired
1. Providing a precomputed alignment and/or tree to SAT´ can
save substantial time. To begin, follow
steps 1
through
6
in the
“Basic Analysis” sections
8.3
and
8.4
. During
step 2
, provide a
FASTA-formatted file with aligned sequences. The “Initial
Alignment” dialog will have the “Use for initial tree” checkbox
enabled. If a user-specified starting tree is available, click the
“Tree file (optional)” button and provide the Newick-
formatted starting tree file name.
2. Proceed with
steps 7
through
10
from the “Basic Analysis”
section.
8.6 Advanced
Analysis: Providing an
Initial Alignment (and/
or Initial Tree)
